rs17207923
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_001365276.2(TNXB):c.5713G>A(p.Glu1905Lys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0223 in 1,612,862 control chromosomes in the GnomAD database, including 658 homozygotes. In-silico tool predicts a benign outcome for this variant. 13/16 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Consequence
NM_001365276.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -20 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TNXB | NM_001365276.2 | c.5713G>A | p.Glu1905Lys | missense_variant | 16/44 | ENST00000644971.2 | |
TNXB | NM_019105.8 | c.5713G>A | p.Glu1905Lys | missense_variant | 16/44 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TNXB | ENST00000644971.2 | c.5713G>A | p.Glu1905Lys | missense_variant | 16/44 | NM_001365276.2 | |||
TNXB | ENST00000647633.1 | c.6454G>A | p.Glu2152Lys | missense_variant | 17/45 | P1 | |||
TNXB | ENST00000375244.7 | c.5713G>A | p.Glu1905Lys | missense_variant | 16/44 | 5 |
Frequencies
GnomAD3 genomes ? AF: 0.0377 AC: 5737AN: 152178Hom.: 170 Cov.: 32
GnomAD3 exomes AF: 0.0211 AC: 5148AN: 244330Hom.: 117 AF XY: 0.0198 AC XY: 2642AN XY: 133704
GnomAD4 exome AF: 0.0207 AC: 30184AN: 1460566Hom.: 488 Cov.: 34 AF XY: 0.0199 AC XY: 14490AN XY: 726582
GnomAD4 genome ? AF: 0.0377 AC: 5735AN: 152296Hom.: 170 Cov.: 32 AF XY: 0.0364 AC XY: 2711AN XY: 74460
ClinVar
Submissions by phenotype
not specified Benign:1
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | - | - - |
Ehlers-Danlos syndrome Benign:1
Benign, criteria provided, single submitter | clinical testing | Genome Diagnostics Laboratory, The Hospital for Sick Children | Jun 02, 2022 | - - |
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | GeneDx | Jul 09, 2018 | - - |
Cardiovascular phenotype Benign:1
Benign, criteria provided, single submitter | clinical testing | Ambry Genetics | Jan 21, 2019 | This alteration is classified as benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at